Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008217.1 Hibiscus syriacus cultivar Beakdansim tig00110847_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2417150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 14
Found at i:1304818 original size:38 final size:38
Alignment explanation
Indices: 1304767--1304840 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
1304757 ATCCTTACCG
1304767 ATCATGAAGATGATCCCAAAGGTTTTTACGCTGGCTAC
1 ATCATGAAGATGATCCCAAAGGTTTTTACGCTGGCTAC
1304805 ATCATGAAGATGATCCCAAAGGTTTTTACGCTGGCT
1 ATCATGAAGATGATCCCAAAGGTTTTTACGCTGGCT
1304841 GATGGAAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (38 bp):
ATCATGAAGATGATCCCAAAGGTTTTTACGCTGGCTAC
Found at i:1309946 original size:11 final size:11
Alignment explanation
Indices: 1309930--1309979 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
1309920 CTTCAGCAGC
1309930 TCATTCTAGAT
1 TCATTCTAGAT
*
1309941 TCATTCTAGAA
1 TCATTCTAGAT
*
1309952 T-ATTC---AC
1 TCATTCTAGAT
1309959 TCATTCTAGAT
1 TCATTCTAGAT
1309970 TCATTCTAGA
1 TCATTCTAGA
1309980 ATATTCACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
7 2 0.06
8 4 0.12
10 4 0.12
11 22 0.69
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (11 bp):
TCATTCTAGAT
Found at i:1309971 original size:29 final size:29
Alignment explanation
Indices: 1309929--1309988 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1309919 ACTTCAGCAG
1309929 CTCATTCTAGATTCATTCTAGAATATTCA
1 CTCATTCTAGATTCATTCTAGAATATTCA
1309958 CTCATTCTAGATTCATTCTAGAATATTCA
1 CTCATTCTAGATTCATTCTAGAATATTCA
1309987 CT
1 CT
1309989 TCAATAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.42
Consensus pattern (29 bp):
CTCATTCTAGATTCATTCTAGAATATTCA
Found at i:1310073 original size:21 final size:21
Alignment explanation
Indices: 1310049--1310089 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1310039 GTACCATAGT
*
1310049 TGGGACGCGGATCTGTATGGA
1 TGGGACGCGAATCTGTATGGA
*
1310070 TGGGACGTGAATCTGTATGG
1 TGGGACGCGAATCTGTATGG
1310090 GGTTTCCGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.41, T:0.27
Consensus pattern (21 bp):
TGGGACGCGAATCTGTATGGA
Found at i:1311079 original size:2 final size:2
Alignment explanation
Indices: 1311072--1311102 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1311062 AATTTTATTT
1311072 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1311103 TAAATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1311285 original size:2 final size:2
Alignment explanation
Indices: 1311278--1311309 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1311268 TATTAGCTAC
1311278 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1311310 TATGTTGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1315753 original size:2 final size:2
Alignment explanation
Indices: 1315659--1315741 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
1315649 TCATATCCGA
1315659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1315701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1315742 ACACAATATA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1316250 original size:25 final size:27
Alignment explanation
Indices: 1316233--1316293 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
1316223 TATAATATTT
* *
1316233 TATATAGTTTTAAAATATAGTAGTATA
1 TATATAGTTTCAAAATATAATAGTATA
* *
1316260 TATATAGTTTCAAAAACAAAATAGTATA
1 TATATAGTTTC-AAAATATAATAGTATA
1316288 TATATA
1 TATATA
1316294 ATATAGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.39
Consensus pattern (27 bp):
TATATAGTTTCAAAATATAATAGTATA
Found at i:1316314 original size:32 final size:29
Alignment explanation
Indices: 1316233--1316449 Score: 131
Period size: 26 Copynumber: 7.6 Consensus size: 29
1316223 TATAATATTT
*
1316233 TATATAGTTTT-AAAAT-ATAGTAGTATA
1 TATATAGTTTTAAAAATAATAGTAATATA
* *
1316260 TATATAGTTTCAAAAACAAAATAGTATATATA
1 TATATAGTTT-TAAAA-ATAATAGTA-ATATA
*
1316292 TAATATAGTTTTAAAAATAA-A-TAACAT-
1 T-ATATAGTTTTAAAAATAATAGTAATATA
*
1316319 TATATAGTTTTTAAAAATAGTA-TAAATATA
1 TATATAG-TTTTAAAAATAATAGT-AATATA
*
1316349 TCATTATAGTTTTGAAAATAATATAGTATATATA
1 T-A-TATAGTTTTAAAAAT-A-ATAGTA-ATATA
*
1316383 TATATAGTTTT-GAAATAAT--T-ATAT-
1 TATATAGTTTTAAAAATAATAGTAATATA
** *
1316407 TATATAGTTTTGGGAAGT-A-AGT-ATATA
1 TATATAGTTTT-AAAAATAATAGTAATATA
1316434 T-TATAGTTTTAAAAAT
1 TATATAGTTTTAAAAAT
1316450 GAGTATTAGT
Statistics
Matches: 154, Mismatches: 15, Indels: 44
0.72 0.07 0.21
Matches are distributed among these distances:
24 11 0.07
25 8 0.05
26 24 0.16
27 24 0.16
28 5 0.03
29 11 0.07
30 4 0.03
31 23 0.15
32 24 0.16
33 13 0.08
34 7 0.05
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (29 bp):
TATATAGTTTTAAAAATAATAGTAATATA
Found at i:1316323 original size:33 final size:32
Alignment explanation
Indices: 1316256--1316324 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
1316246 AATATAGTAG
**
1316256 TATATATATAGTTTCAAAAACAAAATAGTATA
1 TATATATATAGTTTCAAAAACAAAATAACATA
* *
1316288 TATATAATATAGTTTTAAAAA-TAAATAACAT-
1 TATAT-ATATAGTTTCAAAAACAAAATAACATA
1316319 TATATA
1 TATATA
1316325 GTTTTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.03
31 5 0.16
32 12 0.38
33 14 0.44
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (32 bp):
TATATATATAGTTTCAAAAACAAAATAACATA
Found at i:1316348 original size:26 final size:26
Alignment explanation
Indices: 1316233--1316349 Score: 78
Period size: 27 Copynumber: 4.2 Consensus size: 26
1316223 TATAATATTT
*
1316233 TATATAGTTTTAAAATATAGTAGT-ATA
1 TATATAGTTTTAAAA-ATAGTA-TAACA
* *
1316260 TATATAGTTTCAAAAACAAAATAGTATATATA
1 TATATAGTTT----TA-AAAATAGTATA-ACA
*
1316292 TAATATAGTTTTAAAAATA-AATAACA
1 T-ATATAGTTTTAAAAATAGTATAACA
1316318 TTATATAGTTTTTAAAAATAGTATAA-A
1 -TATATAG-TTTTAAAAATAGTATAACA
1316345 TATAT
1 TATAT
1316350 CATTATAGTT
Statistics
Matches: 74, Mismatches: 5, Indels: 23
0.73 0.05 0.23
Matches are distributed among these distances:
26 13 0.18
27 26 0.35
28 10 0.14
29 1 0.01
30 1 0.01
31 7 0.09
32 7 0.09
33 9 0.12
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATATAGTTTTAAAAATAGTATAACA
Found at i:1316356 original size:34 final size:34
Alignment explanation
Indices: 1316308--1316393 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 34
1316298 AGTTTTAAAA
*
1316308 ATAAATA-A-CATTATATAGTTTTTAAAAATAGT
1 ATAAATATATCATTATATAGTTTTTAAAAATAAT
*
1316340 ATAAATATATCA-T-TATAG-TTTTGAAAATAAT
1 ATAAATATATCATTATATAGTTTTTAAAAATAAT
*
1316371 AT-AGTATAT-ATATATATAGTTTT
1 ATAAATATATCAT-TATATAGTTTT
1316394 GAAATAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
29 1 0.02
30 6 0.13
31 14 0.31
32 17 0.38
33 5 0.11
34 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (34 bp):
ATAAATATATCATTATATAGTTTTTAAAAATAAT
Found at i:1316549 original size:17 final size:16
Alignment explanation
Indices: 1316527--1316567 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1316517 ATAAATATAG
1316527 TTTTTATTTATATGTCA
1 TTTTTATTTA-ATGTCA
*
1316544 TTTTTATTTAATGTTA
1 TTTTTATTTAATGTCA
*
1316560 TTATTATT
1 TTTTTATT
1316568 AACTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTTTATTTAATGTCA
Found at i:1318206 original size:2 final size:2
Alignment explanation
Indices: 1318199--1318225 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1318189 GTCCCTGTAT
1318199 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1318226 GAATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1322304 original size:46 final size:49
Alignment explanation
Indices: 1322252--1322343 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 49
1322242 TAAATTGTCT
**
1322252 CTATTA-TTAAAAATT-TAAAAATTCAAAATATAT-TTAATTTATAATC
1 CTATTATTTAAAAATTATAAAAATGAAAAATATATATTAATTTATAATC
* **
1322298 CTATTATTTCAAAATTATAATTATGAAAAATATATATTAATTTATA
1 CTATTATTTAAAAATTATAAAAATGAAAAATATATATTAATTTATA
1322344 TATATTTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 6 0.16
47 8 0.21
48 14 0.37
49 10 0.26
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (49 bp):
CTATTATTTAAAAATTATAAAAATGAAAAATATATATTAATTTATAATC
Found at i:1322518 original size:97 final size:97
Alignment explanation
Indices: 1322340--1322519 Score: 238
Period size: 97 Copynumber: 1.9 Consensus size: 97
1322330 TATATTAATT
* * * *
1322340 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATAACTTCTAGGTGTCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATAACATCCAGGTATCT
*
1322405 TAAGACAGCTCTTTTCTTTGATATTTAAAAAA
66 TAAGACAGCTCCTTTCTTTGATATTTAAAAAA
* * *
1322437 TATATA-ATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTAT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAAT-AACATCCAGGTAT
* *
1322501 TTTAAGACTGC-CCTTTCTT
64 CTTAAGACAGCTCCTTTCTT
1322520 AATATTGGAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
96 6 0.08
97 48 0.68
98 17 0.24
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (97 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATAACATCCAGGTATCT
TAAGACAGCTCCTTTCTTTGATATTTAAAAAA
Found at i:1322651 original size:3 final size:3
Alignment explanation
Indices: 1322643--1322731 Score: 162
Period size: 3 Copynumber: 30.0 Consensus size: 3
1322633 ATGGTTAAAT
1322643 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1322691 ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1322732 TAAAATTAAC
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1323604 original size:13 final size:12
Alignment explanation
Indices: 1323581--1323619 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
1323571 AGTTTCTTTC
1323581 TTCTTTCTTTGTT
1 TTCTTT-TTTGTT
1323594 TTCTGTTTTTGTT
1 TTCT-TTTTTGTT
1323607 TTCTTTTTT-TT
1 TTCTTTTTTGTT
1323618 TT
1 TT
1323620 ACTCTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.16
12 5 0.20
13 14 0.56
14 2 0.08
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (12 bp):
TTCTTTTTTGTT
Found at i:1323891 original size:16 final size:15
Alignment explanation
Indices: 1323870--1323899 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1323860 GCCCCGTGGT
1323870 CCCTAGGGTATTATTA
1 CCCTAGGGT-TTATTA
1323886 CCCTAGGGTTTATT
1 CCCTAGGGTTTATT
1323900 CTGGATGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
CCCTAGGGTTTATTA
Found at i:1324062 original size:3 final size:3
Alignment explanation
Indices: 1324054--1324113 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
1324044 GGCCTGTTTG
* *
1324054 TAA TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
1324100 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
1324114 TAAATAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1324286 original size:22 final size:22
Alignment explanation
Indices: 1324258--1324313 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
1324248 TGTTGAACAG
1324258 GTTCTTCTCATTCTTCAGATGA
1 GTTCTTCTCATTCTTCAGATGA
1324280 GTTCTTCTCATTCTTCAGATGA
1 GTTCTTCTCATTCTTCAGATGA
1324302 GTTCTTCTCATT
1 GTTCTTCTCATT
1324314 ATGAACTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.16, C:0.23, G:0.12, T:0.48
Consensus pattern (22 bp):
GTTCTTCTCATTCTTCAGATGA
Found at i:1324317 original size:16 final size:16
Alignment explanation
Indices: 1324298--1324353 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
1324288 CATTCTTCAG
1324298 ATGAGTTCTTCTCATT
1 ATGAGTTCTTCTCATT
* *
1324314 ATGAACTTCTTCTTCTTCAT
1 ATG-AGTTCTTC-TCAT--T
1324334 ATGAGTTCTTCTCATT
1 ATGAGTTCTTCTCATT
1324350 ATGA
1 ATGA
1324354 ACTCCTTCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 8 0.25
17 7 0.22
18 6 0.19
19 7 0.22
20 4 0.12
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.48
Consensus pattern (16 bp):
ATGAGTTCTTCTCATT
Found at i:1324325 original size:39 final size:38
Alignment explanation
Indices: 1324281--1324362 Score: 123
Period size: 36 Copynumber: 2.2 Consensus size: 38
1324271 TTCAGATGAG
1324281 TTCTTCTCATTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTCTTCTC-TTCTTCAGATGAGTTCTTCTCATTATGAAC
*
1324320 TTC-T-TCTTCTTCATATGAGTTCTTCTCATTATGAAC
1 TTCTTCTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
*
1324356 TCCTTCT
1 TTCTTCT
1324363 GGAAATGCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 31 0.79
37 3 0.08
38 2 0.05
39 3 0.08
ACGTcount: A:0.18, C:0.24, G:0.09, T:0.49
Consensus pattern (38 bp):
TTCTTCTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
Found at i:1324328 original size:20 final size:19
Alignment explanation
Indices: 1324303--1324362 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
1324293 TTCAGATGAG
1324303 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAAC-TC
*
1324323 TTCTTCTTCA-TATG-A--G
1 TTCTTC-TCATTATGAACTC
1324339 TTCTTCTCATTATGAACTCC
1 TTCTTCTCATTATGAACT-C
1324359 TTCT
1 TTCT
1324363 GGAAATGCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 3 0.09
16 10 0.31
17 1 0.03
19 1 0.03
20 14 0.44
21 3 0.09
ACGTcount: A:0.18, C:0.25, G:0.07, T:0.50
Consensus pattern (19 bp):
TTCTTCTCATTATGAACTC
Found at i:1324330 original size:36 final size:36
Alignment explanation
Indices: 1324290--1324362 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1324280 GTTCTTCTCA
*
1324290 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTC
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTC
*
1324326 TTCTTCATATGAGTTCTTCTCATTATGAACTCCTTC
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTC
1324362 T
1 T
1324363 GGAAATGCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (36 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTC
Found at i:1324533 original size:112 final size:111
Alignment explanation
Indices: 1324408--1325077 Score: 775
Period size: 112 Copynumber: 6.0 Consensus size: 111
1324398 AGAGCTATGC
* *
1324408 AAAAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGAT-AAGTTCTTCTTAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTT-TTCTTCTTCTTCAGATGAAGTTCTTCTTAT
** * *
1324472 TATGAATTTTCTCTGAAAAAGTTGATCCATCGAGTGATGAATTTAAACA
64 TATGAATTTTC-CTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCA
* *
1324521 AAAAGTTGAACAAATTCTTCTCATTATGAA--TTTCTTCTTCTTCAGATGACGAGTTATTCTTAT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTCTTCTTCTTCAGATGA--AGTTCTTCTTAT
* * *
1324584 TATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAATTTAAACA
64 TATGAA-TTTTCCTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCA
*
1324633 AAAAGTTGAACAAATTCTTCTCATTATGAA--TTTCTTCTTCTTCAGATGACGAGTTCTTCTTAT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTCTTCTTCTTCAGATGA--AGTTCTTCTTAT
* *
1324696 TATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCA
64 TATGAA-TTTTCCTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCA
* *
1324745 AAAAGATGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATG-AGTTCTTCTCAT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTT-CTTCTTCAGATGAAGTTCTTCTTAT
* * *
1324809 TATGAACTCTT-CTGG-AACTGCTGATCCACCGAGTGATGAATTTAAGCA
64 TATGAA-TTTTCCTGGCAA-TGTTGATCCATCGAGTGATGAATTTAAGCA
* *
1324857 AAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATG-AGTTCTTCTCAT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTT-TTC-TTCTTCTTCAGATGAAGTTCTTCTTAT
* ** * * * *
1324921 TATGAACTCTAACTGGCACTGCTGATCCACCAAGTGATGAATTTAAGCA
64 TATGAA-TTTTCCTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCA
*
1324970 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAA-TTCTTCTAAT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTT-CTTCTTCAGATGAAGTTCTTCTTAT
* ** * * * *
1325034 TATGAACTCTAACTGGAAATGTTGATCCATTGAATGATGGATTT
64 TATGAA-TTTTCCTGGCAATGTTGATCCATCGAGTGATGAATTT
1325078 TAATCTTTGC
Statistics
Matches: 509, Mismatches: 34, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
109 15 0.03
110 2 0.00
111 2 0.00
112 314 0.62
113 156 0.31
114 3 0.01
115 5 0.01
116 12 0.02
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (111 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTCTTCTTCTTCAGATGAAGTTCTTCTTATTA
TGAATTTTCCTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCA
Found at i:1324982 original size:225 final size:224
Alignment explanation
Indices: 1324408--1325062 Score: 885
Period size: 224 Copynumber: 2.9 Consensus size: 224
1324398 AGAGCTATGC
* * *
1324408 AAAAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGATAAGTTCTTCTTATT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTATT
* * ** ** * * *
1324473 ATGAATTTTCTCTGAAAAAGTTGATCCATCGAGTGATGAATTTAAACAAAAAGTTGAACAAATTC
65 ATGAACTCTAACTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTC
* * *
1324538 TTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTATTCTTATTATGAACTCTACCTG
130 TTCTCATTATGAACTTATTCTTCCTTCTTCAGAT---GAGTTCTTCTAATTATGAACTCTAACTG
*
1324599 GCAATGTTGATCCATCGAGTGATGAATTTAAACA
192 G-AATGTTGATCCACCGAGTGATGAATTTAAACA
*
1324633 AAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATGACGAGTTCTTCTTA
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT---GAGTTCTTCTTA
* *
1324695 TTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCAAAAAGATGAACAAGT
63 TTATGAACTCTAACTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGT
* *
1324760 TCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TCTGG
128 TCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTAATTATGAACTCTAACTGG
* *
1324824 AACTGCTGATCCACCGAGTGATGAATTTAAGCA
193 AA-TGTTGATCCACCGAGTGATGAATTTAAACA
* *
1324857 AAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTTATT
* * * *
1324922 ATGAACTCTAACTGGCACTGCTGATCCACCAAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTC
65 ATGAACTCTAACTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTC
*
1324987 TTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAATTCTTCTAATTATGAACTCTAACTGGAA
130 TTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTAATTATGAACTCTAACTGG-A
1325052 ATGTTGATCCA
194 ATGTTGATCCA
1325063 TTGAATGATG
Statistics
Matches: 383, Mismatches: 33, Indels: 27
0.86 0.07 0.06
Matches are distributed among these distances:
221 15 0.04
222 1 0.00
223 2 0.01
224 163 0.43
225 153 0.40
226 15 0.04
227 10 0.03
228 24 0.06
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (224 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTATTA
TGAACTCTAACTGGCAATGTTGATCCATCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCT
TCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTAATTATGAACTCTAACTGGAAT
GTTGATCCACCGAGTGATGAATTTAAACA
Found at i:1325928 original size:114 final size:114
Alignment explanation
Indices: 1325765--1325984 Score: 316
Period size: 114 Copynumber: 1.9 Consensus size: 114
1325755 GATCATGCAG
* * * * * *
1325765 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTTCTACCGAACCAGATCAGATAACTCAAAAA
1 TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTTATACCAAACCAGATCAGATAACTCAAAAA
1325830 AAACTTCCAGAAGATACTATTGGGTCTT-CTTATTTCTACTATGAGCAAA
66 AAACTTCCAGAAGATACTATTGGGT-TTCCTTATTTCTACTATGAGCAAA
* * *
1325879 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTTATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTTATACCAAACCAGATCAGATAACTCAAAAA
* * *
1325944 ACACTTTCAGAAGATGCTATTGGGTTTCCTTATTTCTACTA
66 AAACTTCCAGAAGATACTATTGGGTTTCCTTATTTCTACTA
1325985 CGAGAACGTG
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
113 2 0.02
114 91 0.98
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTTATACCAAACCAGATCAGATAACTCAAAAA
AAACTTCCAGAAGATACTATTGGGTTTCCTTATTTCTACTATGAGCAAA
Found at i:1326700 original size:38 final size:38
Alignment explanation
Indices: 1326658--1326762 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 38
1326648 TTGACCCCCT
1326658 TTTTTCTCTTTTTTTTCTTTTTCTTCTTC-TCTTTTTTC
1 TTTTTCTCTTTTTTTTC-TTTTCTTCTTCTTCTTTTTTC
* *
1326696 TTTTT-TCTTCTTTTTTCTTTTCTTTTTCTTCTTTTTTT
1 TTTTTCTCTT-TTTTTTCTTTTCTTCTTCTTCTTTTTTC
*
1326734 TTCTTTCTCTTTTTTTCCATTTT-TTCTTC
1 TT-TTTCTCTTTTTTTTC-TTTTCTTCTTC
1326763 AAGCATAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
37 14 0.24
38 22 0.38
39 14 0.24
40 8 0.14
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (38 bp):
TTTTTCTCTTTTTTTTCTTTTCTTCTTCTTCTTTTTTC
Found at i:1326701 original size:31 final size:30
Alignment explanation
Indices: 1326656--1326746 Score: 121
Period size: 31 Copynumber: 2.9 Consensus size: 30
1326646 TCTTGACCCC
1326656 CTTTTTTCTCTTTTTTTTCTTTTTCTTCTTCT
1 CTTTTTTCT-TTTTTTTTCTTTTTCTT-TTCT
*
1326688 CTTTTTTCTTTTTTCTTCTTTTTTCTTTTCT
1 CTTTTTTCTTTTTTTTTC-TTTTTCTTTTCT
*
1326719 -TTTTCTTCTTTTTTTTTCTTTCTCTTTT
1 CTTTT-TTCTTTTTTTTTCTTTTTCTTTT
1326747 TTTCCATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
30 13 0.24
31 24 0.44
32 17 0.31
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (30 bp):
CTTTTTTCTTTTTTTTTCTTTTTCTTTTCT
Found at i:1326708 original size:40 final size:37
Alignment explanation
Indices: 1326657--1326762 Score: 126
Period size: 40 Copynumber: 2.8 Consensus size: 37
1326647 CTTGACCCCC
1326657 TTTTTTCTCTTTTTTTTCTTTTTCTTCTTCTCTTTTTTC
1 TTTTTTCTCTTTTTTTTCTTTTT-TTCTTCT-TTTTTTC
1326696 TTTTTTCTTCTTTTTTCTT-TTCTTTTTCTTCTTTTTTT-
1 TTTTTTC-TCTTTTTT-TTCTT-TTTTTCTTCTTTTTTTC
* * *
1326734 TTCTTTCTCTTTTTTTCCATTTTTTCTTC
1 TTTTTTCTCTTTTTTTTCTTTTTTTCTTC
1326763 AAGCATAATA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
36 10 0.17
37 9 0.15
38 6 0.10
39 13 0.22
40 17 0.28
41 5 0.08
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (37 bp):
TTTTTTCTCTTTTTTTTCTTTTTTTCTTCTTTTTTTC
Found at i:1326719 original size:37 final size:39
Alignment explanation
Indices: 1326656--1326748 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 39
1326646 TCTTGACCCC
*
1326656 CTTTTTTCTCTTTTTTTTCTTTTTCTTCTTC-TCTTTTTT
1 CTTTTTTCT-TCTTTTTTCTTTTTCTTCTTCTTCTTTTTT
*
1326695 CTTTTTTCTTCTTTTTTC-TTTTCTTTTTCTTCTTTTTT
1 CTTTTTTCTTCTTTTTTCTTTTTCTTCTTCTTCTTTTTT
1326733 -TTTCTTTC-TCTTTTTT
1 CTTT-TTTCTTCTTTTTT
1326749 TCCATTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
37 21 0.42
38 20 0.40
39 9 0.18
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (39 bp):
CTTTTTTCTTCTTTTTTCTTTTTCTTCTTCTTCTTTTTT
Found at i:1326748 original size:14 final size:13
Alignment explanation
Indices: 1326666--1326750 Score: 70
Period size: 14 Copynumber: 6.5 Consensus size: 13
1326656 CTTTTTTCTC
1326666 TTTTT-TTTCTTT
1 TTTTTCTTTCTTT
*
1326678 TTCTTCTTCTCTTT
1 TTTTTCTT-TCTTT
*
1326692 TTTCTTTTTTCTTCT
1 TTT-TTCTTTCTT-T
*
1326707 TTTTTC-TT-TTC
1 TTTTTCTTTCTTT
1326718 TTTTTC-TTCTTTT
1 TTTTTCTTTC-TTT
1326731 TTTTTCTTTCTCTT
1 TTTTTCTTTCT-TT
1326745 TTTTTC
1 TTTTTC
1326751 CATTTTTTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
11 8 0.14
12 6 0.10
13 13 0.22
14 24 0.41
15 8 0.14
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTCTTT
Found at i:1326756 original size:23 final size:24
Alignment explanation
Indices: 1326666--1326761 Score: 75
Period size: 24 Copynumber: 4.3 Consensus size: 24
1326656 CTTTTTTCTC
*
1326666 TTTT-TTTTCTTTTTCTTCT--TC
1 TTTTCTTTTCTTTTTCTTCTCATT
*
1326687 TCTT-TTTTC-TTTT-TTCTTC-TT
1 TTTTCTTTTCTTTTTCTTC-TCATT
**
1326708 TTTTCTTTTCTTTTTCTTCTTTTT
1 TTTTCTTTTCTTTTTCTTCTCATT
1326732 TTTTCTTTCTCTTTTT-TTC-CATT
1 TTTTCTTT-TCTTTTTCTTCTCATT
1326755 TTTTCTT
1 TTTTCTT
1326762 CAAGCATAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
19 3 0.05
20 5 0.08
21 12 0.19
22 5 0.08
23 14 0.23
24 16 0.26
25 7 0.11
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTCTTTTCTTTTTCTTCTCATT
Found at i:1334381 original size:12 final size:12
Alignment explanation
Indices: 1334364--1334397 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1334354 ATACCATATT
1334364 ACTTCTTTCTCC
1 ACTTCTTTCTCC
*
1334376 ACTTCTTTTTCC
1 ACTTCTTTCTCC
1334388 ACTTCTTTCT
1 ACTTCTTTCT
1334398 ACAAAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.35, G:0.00, T:0.56
Consensus pattern (12 bp):
ACTTCTTTCTCC
Found at i:1337810 original size:45 final size:49
Alignment explanation
Indices: 1337759--1337849 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
1337749 TAAATTGTCT
*
1337759 CTATTA-TTAAAAATTA-AA-AATTAAAAATATAT-TTAATTTATAATC
1 CTATTATTTAAAAATTATAATAATGAAAAATATATATTAATTTATAATC
* *
1337804 CTATTATTTCAAAATTATAATTATGAAAAATATATATTAATTTATA
1 CTATTATTTAAAAATTATAATAATGAAAAATATATATTAATTTATA
1337850 TATATTTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
45 6 0.15
46 9 0.23
47 2 0.05
48 12 0.31
49 10 0.26
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (49 bp):
CTATTATTTAAAAATTATAATAATGAAAAATATATATTAATTTATAATC
Found at i:1337958 original size:16 final size:16
Alignment explanation
Indices: 1337931--1337970 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1337921 CTTTTCTTTG
1337931 ATAT-TTTA-AAAAT-
1 ATATATTTATAAAATA
1337944 ATATAATTTATAAAATA
1 ATAT-ATTTATAAAATA
1337961 ATATATTTAT
1 ATATATTTAT
1337971 GTATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.17
15 4 0.17
16 11 0.48
17 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATTTATAAAATA
Found at i:1338148 original size:3 final size:3
Alignment explanation
Indices: 1338140--1338187 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
1338130 TTTATGGTTA
* * *
1338140 AAT AAT AAT AAT AAT AGT AAT AAT AGT AAT AAT AGT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1338187 A
1 A
1338188 TAAAATTAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1338154 original size:9 final size:9
Alignment explanation
Indices: 1338140--1338182 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
1338130 TTTATGGTTA
*
1338140 AATAATAAT
1 AATAATAGT
1338149 AATAATAGT
1 AATAATAGT
1338158 AATAATAGT
1 AATAATAGT
1338167 AATAATAGT
1 AATAATAGT
1338176 AATAATA
1 AATAATA
1338183 AAATATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (9 bp):
AATAATAGT
Found at i:1339522 original size:3 final size:3
Alignment explanation
Indices: 1339514--1339573 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
1339504 GGCCTGTTTG
* *
1339514 TAA TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
1339560 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
1339574 TAAATAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1348163 original size:131 final size:131
Alignment explanation
Indices: 1347927--1348171 Score: 298
Period size: 131 Copynumber: 1.9 Consensus size: 131
1347917 ATTTGGTCTT
* *
1347927 CCCTAAAGAGTAACAGAGCATATCCTCATTTTTCAGATTTGATCTTTCTGAAAATCAGCGAAGCA
1 CCCTAAAGAGTAACAGAGCATATCCTCATTTTCCAAATTTGATCTTTCTGAAAATCAGCGAAGCA
* * ** * *
1347992 AGTCAACCTCGATTTAATGTTTCCTAAAAAATAGTGAATTGAATCAAAATTCCTGAGTGTGATCT
66 AATCAACCTCGATTCAATCCTTCCTAAAAAATAGTAAATTGAATAAAAATTCCTGAGTGTGATCT
1348057 C
131 C
* * * * *
1348058 CCCTAAAGAGTAGCATAGTATATCCTCATTTTCCCAAATCTT-ATCTTTCTGAAGA-CAGTGAAG
1 CCCTAAAGAGTAACAGAGCATATCCTCATTTT-CCAAAT-TTGATCTTTCTGAAAATCAGCGAAG
* * *
1348121 CAAATCAACTTCGATTCAA-CCTTCATTGAAAAATAGTAAATTGAATAAAAA
64 CAAATCAACCTCGATTCAATCCTTC-CTAAAAAATAGTAAATTGAATAAAAA
1348172 AATCAAGATC
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
130 3 0.03
131 74 0.78
132 16 0.17
133 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (131 bp):
CCCTAAAGAGTAACAGAGCATATCCTCATTTTCCAAATTTGATCTTTCTGAAAATCAGCGAAGCA
AATCAACCTCGATTCAATCCTTCCTAAAAAATAGTAAATTGAATAAAAATTCCTGAGTGTGATCT
C
Found at i:1351306 original size:60 final size:60
Alignment explanation
Indices: 1351229--1351366 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 60
1351219 AACATGATGA
* * * * *
1351229 ATAGTCAATTGAACATTTTGTAACTTTTAATAGTCGAGGAAGTCAACAAAGCAATACCCT
1 ATAGTCAATGGAACATTTAGTAACTTTTAATAATCGAGGAACTCAACAAAACAATACCCT
* * * **
1351289 ATAGTCAATGGATCATTTAGTAATTTTTAATAATCGAGGGACTCAACAAAACAATATGCT
1 ATAGTCAATGGAACATTTAGTAACTTTTAATAATCGAGGAACTCAACAAAACAATACCCT
* *
1351349 ATAGTCAGTGGACCATTT
1 ATAGTCAATGGAACATTT
1351367 GTGTTCTTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (60 bp):
ATAGTCAATGGAACATTTAGTAACTTTTAATAATCGAGGAACTCAACAAAACAATACCCT
Found at i:1356217 original size:20 final size:19
Alignment explanation
Indices: 1356184--1356233 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
1356174 TAATTAGATT
*
1356184 TTTAAATTACATTAATATG
1 TTTAAATTAAATTAATATG
*
1356203 TTTATAATTAAATTAATATAT
1 TTTA-AATTAAATTAATAT-G
1356224 TTTAAATTAA
1 TTTAAATTAA
1356234 TGTATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 4 0.15
20 19 0.70
21 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAAATTAAATTAATATG
Found at i:1356489 original size:23 final size:22
Alignment explanation
Indices: 1356461--1356508 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1356451 AAGGATTTAT
1356461 TTAAAATCAAATATTAATTAAAA
1 TTAAAATCAAATATTAA-TAAAA
** *
1356484 TTAAAATTTAATTTTAATAAAA
1 TTAAAATCAAATATTAATAAAA
1356506 TTA
1 TTA
1356509 TAATTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAATCAAATATTAATAAAA
Found at i:1356494 original size:17 final size:16
Alignment explanation
Indices: 1356455--1356515 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
1356445 AAATATAAGG
* *
1356455 ATTTATTTAAAATCAA
1 ATTTAATTAAAATAAA
1356471 ATATTAATTAAAATTAAA
1 AT-TTAATTAAAA-TAAA
**
1356489 ATTTAATTTTAATAAA
1 ATTTAATTAAAATAAA
1356505 ATTATAATTAA
1 ATT-TAATTAA
1356516 TTTATAATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
16 9 0.25
17 22 0.61
18 5 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTAATTAAAATAAA
Found at i:1356507 original size:22 final size:21
Alignment explanation
Indices: 1356474--1356523 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 21
1356464 AAATCAAATA
1356474 TTAATTAAAATTAAAATTTAATT
1 TTAA-TAAAATTAAAA-TTAATT
*
1356497 TTAATAAAATTATAATTAATT
1 TTAATAAAATTAAAATTAATT
1356518 TATAAT
1 T-TAAT
1356524 TCTTTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 14 0.56
23 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATAAAATTAAAATTAATT
Found at i:1356803 original size:9 final size:9
Alignment explanation
Indices: 1356786--1356866 Score: 81
Period size: 9 Copynumber: 9.0 Consensus size: 9
1356776 ACTTGTTTGG
*
1356786 ATCAACATC
1 ATCATCATC
1356795 ATCATCATC
1 ATCATCATC
1356804 ATCATCATC
1 ATCATCATC
*
1356813 ATCGTCATC
1 ATCATCATC
*
1356822 ATCTTCATC
1 ATCATCATC
* * *
1356831 TTCAGCTTC
1 ATCATCATC
*
1356840 ATCGTCATC
1 ATCATCATC
*
1356849 ATCATCGTC
1 ATCATCATC
*
1356858 ATCTTCATC
1 ATCATCATC
1356867 GTCAGCTTCA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 57 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (9 bp):
ATCATCATC
Found at i:1356867 original size:12 final size:12
Alignment explanation
Indices: 1356791--1356883 Score: 87
Period size: 12 Copynumber: 7.8 Consensus size: 12
1356781 TTTGGATCAA
*
1356791 CATCATCATCAT
1 CATCATCATCTT
*
1356803 CATCATCATCAT
1 CATCATCATCTT
*
1356815 CGTCATCATCTT
1 CATCATCATCTT
* *
1356827 CATCTTCAGCTT
1 CATCATCATCTT
* *
1356839 CATCGTCATCAT
1 CATCATCATCTT
*
1356851 CATCGTCATCTT
1 CATCATCATCTT
* *
1356863 CATCGTCAGCTT
1 CATCATCATCTT
*
1356875 CATCTTCAT
1 CATCATCAT
1356884 TGACCGCTTG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 69 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (12 bp):
CATCATCATCTT
Found at i:1356877 original size:18 final size:18
Alignment explanation
Indices: 1356791--1356883 Score: 89
Period size: 18 Copynumber: 5.2 Consensus size: 18
1356781 TTTGGATCAA
* * *
1356791 CATCATCATCATCATCAT
1 CATCATCAGCTTCATCTT
*
1356809 CATCATC-GTCATCATCTT
1 CATCATCAG-CTTCATCTT
* *
1356827 CATCTTCAGCTTCATCGT
1 CATCATCAGCTTCATCTT
* *
1356845 CATCATCATCGTCATCTT
1 CATCATCAGCTTCATCTT
*
1356863 CATCGTCAGCTTCATCTT
1 CATCATCAGCTTCATCTT
1356881 CAT
1 CAT
1356884 TGACCGCTTG
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
18 60 0.98
19 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (18 bp):
CATCATCAGCTTCATCTT
Found at i:1356883 original size:6 final size:6
Alignment explanation
Indices: 1356786--1356866 Score: 81
Period size: 6 Copynumber: 13.5 Consensus size: 6
1356776 ACTTGTTTGG
* * * *
1356786 ATCAAC ATCATC ATCATC ATCATC ATCATC GTCATC ATCTTC ATCTTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * * * *
1356834 AGCTTC ATCGTC ATCATC ATCGTC ATCTTC ATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATC
1356867 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (6 bp):
ATCATC
Found at i:1359356 original size:200 final size:199
Alignment explanation
Indices: 1358341--1359510 Score: 2053
Period size: 199 Copynumber: 5.9 Consensus size: 199
1358331 TTTAAATTAG
1358341 TATCGACACAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1358405 CTTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
* * *
1358469 CGACAC-TTTTATATATGGATCGACACCTTATGGTTGCACACTG-TTTCCATTCATTATGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
1358532 AAAA
196 AAAA
**** * ** *
1358536 TATCGACACTTTTTTTAAATGGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTAT
1 TATCGACAC-AAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1358601 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGA
65 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGA
*
1358666 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1358731 AAAAA
195 AAAAA
**** * **
1358736 TATCGACACTTTTTTAAATGGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1358801 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
1358866 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
1358931 AAAA
196 AAAA
*
1358935 TATCGACATAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1359000 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
1359065 C-ACCACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 CGA-CACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1359129 AAAAA
195 AAAAA
1359134 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1359199 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTTGGGA
*
1359264 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTATGGACC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
1359329 AAAAA
195 AAAAA
1359334 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
1359399 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTTGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTTGGGA
* *
1359464 TCGACACTTTTTATAAATGGTTCGACACTTTATGGTTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
1359511 GGCCATATTG
Statistics
Matches: 941, Mismatches: 26, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
195 9 0.01
196 1 0.00
197 65 0.07
198 53 0.06
199 524 0.56
200 288 0.31
201 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
AAAA
Found at i:1359677 original size:19 final size:19
Alignment explanation
Indices: 1359631--1359679 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1359621 TTATATTCAC
*
1359631 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1359650 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1359669 ATACAAAATTA
1 ATACAAAATTA
1359680 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1361498 original size:33 final size:33
Alignment explanation
Indices: 1361461--1361526 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1361451 CATCTTAATA
*
1361461 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1361494 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1361527 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1361585 original size:21 final size:21
Alignment explanation
Indices: 1361560--1361603 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1361550 CCCCTTATGC
1361560 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
1361581 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
1361602 CT
1 CT
1361604 TTATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:1364096 original size:175 final size:175
Alignment explanation
Indices: 1363766--1364227 Score: 546
Period size: 175 Copynumber: 2.6 Consensus size: 175
1363756 ACTACTTACG
* * * *
1363766 AAGTATCGACACTTTCAATATGTCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGTTTTT
1 AAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCG--TTT
* *
1363831 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTAAAGTATCGACACATTAT
64 TTATCATATTTTTACCTG-TATAT--TTTTGGATCGATACATTTTTTAAAGTATCGACACATTAT
* *
1363896 AGGCGCTAATGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T-
126 AGGCACTAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTA
* *
1363944 AAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGG-TTTATCATTTTGATACCGATTTT
1 AAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGTTTTT
*
1364008 ATCATATTTTTACCTGGTATATTATTTGGATCGATACATTTTTTAAAGTA-CGACACTTTATAGG
66 ATCATATTTTTACCT-GTATATT-TTTGGATCGATACATTTTTTAAAGTATCGACACATTATAGG
* *
1364072 -ATTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTA
129 CACT--AA-TGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTA
* * * *
1364121 AAGTACCGACAC-TTAAATGTATCC-GTAGCGCTTTACCGGTTTTATCATTTCT-ATACCGGTTT
1 AAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACC-GTTT
* * *
1364183 TTGTCATAGTTTTACCAT-TATATCGTTTTGGATCGACACATTTTT
64 TTATCATATTTTTACC-TGTATAT--TTTTGGATCGATACATTTTT
1364228 AATATTAATT
Statistics
Matches: 250, Mismatches: 21, Indels: 27
0.84 0.07 0.09
Matches are distributed among these distances:
172 1 0.00
173 14 0.06
174 26 0.10
175 73 0.29
176 32 0.13
177 65 0.26
178 39 0.16
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (175 bp):
AAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGTTTTT
ATCATATTTTTACCTGTATATTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATAGGCA
CTAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTA
Found at i:1366026 original size:51 final size:51
Alignment explanation
Indices: 1365950--1366051 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
1365940 TGGGATAGAA
1365950 ACCCTAATTGGGTTTAGGGTTACACATTTGGGCCTCCGGGTTGGGCTCTTG
1 ACCCTAATTGGGTTTAGGGTTACACATTTGGGCCTCCGGGTTGGGCTCTTG
1366001 ACCCTAATTGGGTTTAGGGTTACACATTTGGGCCTCCGGGTTGGGCTCTTG
1 ACCCTAATTGGGTTTAGGGTTACACATTTGGGCCTCCGGGTTGGGCTCTTG
1366052 GTTCTGGGCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (51 bp):
ACCCTAATTGGGTTTAGGGTTACACATTTGGGCCTCCGGGTTGGGCTCTTG
Found at i:1366095 original size:3 final size:3
Alignment explanation
Indices: 1366087--1366195 Score: 127
Period size: 3 Copynumber: 36.0 Consensus size: 3
1366077 GTTAGGTTTT
*
1366087 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
1366133 T-A TAA T-A TAA TAA TAA TAA TAAA TAAA TAAA TAAA TAA -AA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA T-AA T-AA T-AA T-AA TAA TAA TAA TAA
1366179 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
1366196 AAAAAACCAA
Statistics
Matches: 96, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
2 8 0.08
3 70 0.73
4 18 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1366641 original size:84 final size:84
Alignment explanation
Indices: 1366500--1366691 Score: 298
Period size: 84 Copynumber: 2.3 Consensus size: 84
1366490 TTTCCAGATG
* * * * *
1366500 AGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGATGTTGATCTATCTTCTTCTGTGATAGCG
1 AGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATGCTAATCTATCTTCTTCTGTGATAGAG
1366565 TCGAGCAAAAGGTTGAACA
66 TCGAGCAAAAGGTTGAACA
1366584 AGTTCTTCTCATTATGAACTTCTTCTGGAAAAG-TGTATGCTAATCTATC-TCTTTCTGTGATAG
1 AGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTG-ATGCTAATCTATCTTC-TTCTGTGATAG
*
1366647 AGTCTAGCAAAAGGTTGAACA
64 AGTCGAGCAAAAGGTTGAACA
1366668 AGTTCTTCTCATTATGAACTTCTT
1 AGTTCTTCTCATTATGAACTTCTT
1366692 ATTCCTCTTT
Statistics
Matches: 100, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
83 4 0.04
84 96 0.96
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (84 bp):
AGTTCTTCTCATTATGAACTTCTTCTGGAAAAGTTGATGCTAATCTATCTTCTTCTGTGATAGAG
TCGAGCAAAAGGTTGAACA
Found at i:1366723 original size:123 final size:123
Alignment explanation
Indices: 1366583--1366971 Score: 681
Period size: 123 Copynumber: 3.2 Consensus size: 123
1366573 AAGGTTGAAC
* *
1366583 AAGTTCTTCTCATTATGAAC-TTCTTCTGGAAAAGTGTATGCTAATCTATCTCTTTCTGTGATAG
1 AAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGTGTATGTTAATCTATCTCCTTCTGTGATAG
*
1366647 AGTCTAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTCTTTAGAT
65 AGTCTAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTCTTCAGAT
*
1366706 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGTATGTTTATCTATCTCCTTCTGTGATAGA
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGTATGTTAATCTATCTCCTTCTGTGATAGA
* * *
1366771 TTCTAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTCCTTCTTCCTCTTCAGAT
66 GTCTAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTCTTCAGAT
* *
1366829 AAGTTCTTCTCATTGTGAACTTTCTCTGGAAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGA
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGTATGTTAATCTATCTCCTTCTGTGATAGA
1366894 GTCTAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTCTTCAGAT
66 GTCTAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTCTTCAGAT
1366952 AAGTTCTTCTCATTATGAAC
1 AAGTTCTTCTCATTATGAAC
1366972 ACTTCTGGAA
Statistics
Matches: 252, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
123 249 0.99
124 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
AAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGTATGTTAATCTATCTCCTTCTGTGATAGA
GTCTAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTCTTCAGAT
Found at i:1366724 original size:207 final size:208
Alignment explanation
Indices: 1366420--1366816 Score: 534
Period size: 207 Copynumber: 1.9 Consensus size: 208
1366410 GATGACAATT
** *
1366420 TATCTCATTCTGTGATGTAATCTATTAAAAAGTTAAACAAATTCTTTTCATTATGAACTTCTTCT
1 TATCTCATTCTGTGATGTAATCTAGCAAAAAGTTAAACAAATTCTTCTCATTATGAACTTCTTCT
* * * *
1366485 CTTTTTTTCCAGATGAGTTCTTCTCATTATGAACTC-CTTCTGGAAATGT-TGATGTTGATCTAT
66 CTCTCTTT-CAGATAAGTTCTTCTCATTATGAACTCTC-TCTGGAAAAGTGT-ATGTTGATCTAT
* * *
1366548 CTTCTTCTGTGATAGCGTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTGGA
128 CTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTCCTTCTGGA
1366613 AAAGTGTATGCTAATC
193 AAAGTGTATGCTAATC
* * * * * *
1366629 TATCTCTTTCTGTGATAG-AGTCTAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTA
1 TATCTCATTCTGTGAT-GTAATCTAGCAAAAAGTTAAACAAATTCTTCTCATTATGAACTTCTTC
* *
1366693 T-TCCTCTTT-AGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGTATGTTTATCTATC
65 TCT-CTCTTTCAGATAAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTGTATGTTGATCTATC
* *
1366756 TCCTTCTGTGATAGATTCTAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTCCTTCT
129 TCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTCCTTCT
1366817 TCCTCTTCAG
Statistics
Matches: 164, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
207 102 0.62
208 3 0.02
209 58 0.35
210 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (208 bp):
TATCTCATTCTGTGATGTAATCTAGCAAAAAGTTAAACAAATTCTTCTCATTATGAACTTCTTCT
CTCTCTTTCAGATAAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTGTATGTTGATCTATCTC
CTTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTCCTTCTGGAAAA
GTGTATGCTAATC
Found at i:1368253 original size:18 final size:19
Alignment explanation
Indices: 1368230--1368273 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
1368220 TATATAAAAG
1368230 AATAAATTGAATTTC-AAA
1 AATAAATTGAATTTCGAAA
*
1368248 AATAAATTTAATTTCGAAA
1 AATAAATTGAATTTCGAAA
1368267 AGATAAA
1 A-ATAAA
1368274 CTTGGAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (19 bp):
AATAAATTGAATTTCGAAA
Found at i:1380178 original size:14 final size:14
Alignment explanation
Indices: 1380161--1380189 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1380151 TAATATGACT
1380161 AAAATAATAATTAA
1 AAAATAATAATTAA
1380175 AAAATAATAATTAA
1 AAAATAATAATTAA
1380189 A
1 A
1380190 CATACTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATAATAATTAA
Found at i:1381679 original size:3 final size:3
Alignment explanation
Indices: 1381671--1381747 Score: 104
Period size: 3 Copynumber: 25.3 Consensus size: 3
1381661 TTGGACTTGT
1381671 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATAA ATAA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A AT-A ATA ATA
*
1381718 ATA ATG ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1381748 AAAAAACTAA
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
2 4 0.06
3 54 0.78
4 11 0.16
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1381971 original size:34 final size:34
Alignment explanation
Indices: 1381933--1382009 Score: 145
Period size: 34 Copynumber: 2.3 Consensus size: 34
1381923 AATAATAATA
*
1381933 TCATAAATTTTCTATAAAAGAAACCCCACAAAAT
1 TCATAAATCTTCTATAAAAGAAACCCCACAAAAT
1381967 TCATAAATCTTCTATAAAAGAAACCCCACAAAAT
1 TCATAAATCTTCTATAAAAGAAACCCCACAAAAT
1382001 TCATAAATC
1 TCATAAATC
1382010 CCCTAAATCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.26
Consensus pattern (34 bp):
TCATAAATCTTCTATAAAAGAAACCCCACAAAAT
Found at i:1384094 original size:2 final size:2
Alignment explanation
Indices: 1384087--1384120 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1384077 AATAGGTCAA
1384087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1384121 TTGAAAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1388713 original size:20 final size:21
Alignment explanation
Indices: 1388684--1388757 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 21
1388674 ACAGCCTTCG
*
1388684 TGCATGGATGCACA-ACAGGA
1 TGCATCGATGCACAGACAGGA
* **
1388704 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAGACAGGA
1388725 TGCATCGATGCACAGA-AGGA
1 TGCATCGATGCACAGACAGGA
*
1388745 TGCATCGAGGCAC
1 TGCATCGATGCAC
1388758 TATTTGCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 27 0.60
21 18 0.40
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (21 bp):
TGCATCGATGCACAGACAGGA
Found at i:1388719 original size:41 final size:41
Alignment explanation
Indices: 1388674--1388757 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 41
1388664 CTAGCAGGTT
* *
1388674 ACAGCCTTCG-TGCATGGATGCACA-ACAGGATGCATCGATGC
1 ACAGCCTT-GATGCATCGATGCACAGA-AGGATGCATCGAGGC
1388715 ACAGCCTTGATGCATCGATGCACAGAAGGATGCATCGAGGC
1 ACAGCCTTGATGCATCGATGCACAGAAGGATGCATCGAGGC
1388756 AC
1 AC
1388758 TATTTGCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 1 0.03
41 37 0.95
42 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (41 bp):
ACAGCCTTGATGCATCGATGCACAGAAGGATGCATCGAGGC
Found at i:1388824 original size:42 final size:41
Alignment explanation
Indices: 1388778--1388876 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
1388768 CGGTGTTTGA
*
1388778 GTGCATGGATGCACTGCA-TGATGCATCGATACACTAGTGCA-G
1 GTGCATGGATGCACTGCAGGGATGCATCGATACAC---TGCAGG
* *
1388820 GTGCATGGATGCACTGCAGGGATGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGGATGCATCGATACACTGCA-GG
1388862 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1388877 TTAACACCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 4 0.08
42 34 0.67
43 13 0.25
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.22
Consensus pattern (41 bp):
GTGCATGGATGCACTGCAGGGATGCATCGATACACTGCAGG
Found at i:1388847 original size:21 final size:20
Alignment explanation
Indices: 1388779--1388876 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 20
1388769 GGTGTTTGAG
*
1388779 TGCATGGATGCACTGCATGA
1 TGCATGGATGCACTGCAGGA
* *
1388799 TGCATCGATACACTAGTGCAGG-
1 TGCATGGATGCAC---TGCAGGA
1388821 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
*
1388842 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCA-GGA
1388863 TGCATGGATGCACT
1 TGCATGGATGCACT
1388877 TTAACACCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 34 0.51
22 11 0.16
23 5 0.07
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.22
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:1388977 original size:29 final size:29
Alignment explanation
Indices: 1388956--1389013 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1388946 AAACTTTGAA
*
1388956 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAACTCCAAAAACA-TTTG
1388985 TAAATTCAATTCAACTCCAAAAATCATTT
1 TAAATTCAATTCAACTCCAAAAA-CATTT
1389014 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAACTCCAAAAACATTTG
Found at i:1389006 original size:30 final size:30
Alignment explanation
Indices: 1388956--1389015 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1388946 AAACTTTGAA
*
1388956 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAACTCCAAAAATCATTTTG
1388985 TAAATTCAATTCAACTCCAAAAATCATTTTG
1 TAAATTCAATT-AACTCCAAAAATCATTTTG
1389016 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAACTCCAAAAATCATTTTG
Found at i:1390331 original size:19 final size:20
Alignment explanation
Indices: 1390288--1390335 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1390278 TCTAAATCCT
*
1390288 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATATCATTTTGG
* *
1390308 CTTTCAAAATAT-ATTTTTG
1 TTTTCAAAATATCATTTTGG
1390327 TTTTCAAAA
1 TTTTCAAAA
1390336 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGG
Found at i:1391645 original size:21 final size:21
Alignment explanation
Indices: 1391621--1391703 Score: 91
Period size: 20 Copynumber: 4.0 Consensus size: 21
1391611 CTAGTCATTG
*
1391621 CAGCCTTCG-TGCATGGATGCA
1 CAGCCTT-GATGCATCGATGCA
**
1391642 CAG-CAGGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
1391662 CAGCCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
**
1391683 CAG-AATGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
1391703 C
1 C
1391704 TAATTACATT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
19 1 0.02
20 31 0.58
21 21 0.40
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (21 bp):
CAGCCTTGATGCATCGATGCA
Found at i:1391659 original size:20 final size:20
Alignment explanation
Indices: 1391630--1391703 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1391620 GCAGCCTTCG
* *
1391630 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCATGA
*
1391650 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-CATGA
*
1391671 TGCATCGATGCACAGAATGA
1 TGCATCGATGCACAGCATGA
1391691 TGCATCGATGCAC
1 TGCATCGATGCAC
1391704 TAATTACATT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 30 0.62
21 18 0.38
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCATGA
Found at i:1391666 original size:41 final size:41
Alignment explanation
Indices: 1391621--1391703 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
1391611 CTAGTCATTG
* *
1391621 CAGCCTTCG-TGCATGGATGCACAGCAGGATGCATCGATGCA
1 CAGCCTT-GATGCATCGATGCACAGAAGGATGCATCGATGCA
*
1391662 CAGCCTTGATGCATCGATGCACAGAATGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1391703 C
1 C
1391704 TAATTACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (41 bp):
CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
Found at i:1391770 original size:42 final size:41
Alignment explanation
Indices: 1391722--1391822 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 41
1391712 TTCGGTGTTT
* *
1391722 GAGTGCATGGATGCACTGTA-TGATGCATCGATGCACT-AG
1 GAGTGCATGGATGCACTGCAGGGATGCATCGATGCACTCAG
*
1391761 TGCAGGTGCATGGATGCACTGCAGGGATGCATGGATGCACTCCAG
1 -G-A-GTGCATGGATGCACTGCAGGGATGCATCGATGCACT-CAG
1391806 GAGTGCATGGATGCACT
1 GAGTGCATGGATGCACT
1391823 TTGACACCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
40 1 0.02
41 1 0.02
42 32 0.60
43 16 0.30
44 1 0.02
45 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.23
Consensus pattern (41 bp):
GAGTGCATGGATGCACTGCAGGGATGCATCGATGCACTCAG
Found at i:1391793 original size:21 final size:20
Alignment explanation
Indices: 1391725--1391822 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 20
1391715 GGTGTTTGAG
* *
1391725 TGCATGGATGCACTGTATGA
1 TGCATGGATGCACTGCAGGA
*
1391745 TGCATCGATGCACTAGTGCAGG-
1 TGCATGGATGCAC---TGCAGGA
1391767 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
*
1391788 TGCATGGATGCACTCCAGGA
1 TGCATGGATGCACTGCAGGA
1391808 GTGCATGGATGCACT
1 -TGCATGGATGCACT
1391823 TTGACACCCT
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.06
20 17 0.25
21 30 0.45
22 12 0.18
23 4 0.06
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.23
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:1391923 original size:29 final size:30
Alignment explanation
Indices: 1391891--1391959 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
1391881 GAAACCTTTT
1391891 AAAAC-TTTGAATAAATTCAATT-AAGTCCA
1 AAAACATTT-AATAAATTCAATTCAAGTCCA
*
1391920 AAAACATTTTATAAATTCAATTCAAGTCCA
1 AAAACATTTAATAAATTCAATTCAAGTCCA
1391950 AAAACCATTT
1 AAAA-CATTT
1391960 TTCCTTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 17 0.47
30 14 0.39
31 5 0.14
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAACATTTAATAAATTCAATTCAAGTCCA
Found at i:1391949 original size:30 final size:30
Alignment explanation
Indices: 1391901--1391960 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
1391891 AAAACTTTGA
1391901 ATAAATTCAATTAAGTCCAAAAA-CATTTT
1 ATAAATTCAATTAAGTCCAAAAACCATTTT
1391930 ATAAATTCAATTCAAGTCCAAAAACCATTTT
1 ATAAATTCAATT-AAGTCCAAAAACCATTTT
1391961 TCCTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 12 0.41
30 11 0.38
31 6 0.21
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (30 bp):
ATAAATTCAATTAAGTCCAAAAACCATTTT
Found at i:1395660 original size:22 final size:22
Alignment explanation
Indices: 1395615--1395671 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1395605 TTTAACCGGC
* *
1395615 CTGACCGTTGACCGTTGATTGGT
1 CTGACAGTTGA-CGTTGATCGGT
*
1395638 CTGACAGTTGACTTTGATCGGT
1 CTGACAGTTGACGTTGATCGGT
*
1395660 CTGACTGTTGAC
1 CTGACAGTTGAC
1395672 CATTGACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (22 bp):
CTGACAGTTGACGTTGATCGGT
Found at i:1397119 original size:65 final size:65
Alignment explanation
Indices: 1397001--1397127 Score: 186
Period size: 65 Copynumber: 2.0 Consensus size: 65
1396991 TGCACTAAGG
* *
1397001 GTGCATCGATGCATAAATTGCATTCGATGTTTCAAACAAGTCTGGAGTACATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAAAGTCTGGAGTACATCGATGCATGGTAT
* *
1397066 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAAATAG-CT-GAGGTGCATCGATGCATGG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAA-AGTCTGGA-GTACATCGATGCATGG
1397128 CTTATGCATC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
64 2 0.04
65 52 0.93
66 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAAAGTCTGGAGTACATCGATGCATGGTAT
Found at i:1397150 original size:65 final size:64
Alignment explanation
Indices: 1397002--1397150 Score: 160
Period size: 65 Copynumber: 2.3 Consensus size: 64
1396992 GCACTAAGGG
* * *
1397002 TGCATCGATGCATAAATTGCATTCGATGTTTCAAACAAGTCTGGAGTACATCGATGCATGGTATG
1 TGCATCGATACATAAA-TGCATTCGATGTTTCAAAAAAGTCTGGAGTACATCGATGCATGGTATA
* * *
1397067 TGCATCGATGCATAAAATGCATTCGATGTTTTAAAAATAG-CT-GAGGTGCATCGATGCATGGCT
1 TGCATCGATACAT-AAATGCATTCGATGTTTCAAAAA-AGTCTGGA-GTACATCGATGCATGG-T
1397130 -TA
62 ATA
*
1397132 TGCATCGGTACACTAAATG
1 TGCATCGATACA-TAAATG
1397151 AATTTGAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
64 2 0.03
65 64 0.88
66 7 0.10
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (64 bp):
TGCATCGATACATAAATGCATTCGATGTTTCAAAAAAGTCTGGAGTACATCGATGCATGGTATA
Found at i:1397840 original size:26 final size:26
Alignment explanation
Indices: 1397775--1397846 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 26
1397765 AAGATAAAAA
* * *
1397775 TTCAAACAAACCAAATATATAT-TAAG
1 TTCAAAC-ATCCAAACATAAATATAAG
*
1397801 TTCAAATATCCAAACATAAATATAAG
1 TTCAAACATCCAAACATAAATATAAG
* * *
1397827 TTCAAGCATTCAAACTTAAA
1 TTCAAACATCCAAACATAAA
1397847 CATCCAAACA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 11 0.30
26 26 0.70
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (26 bp):
TTCAAACATCCAAACATAAATATAAG
Found at i:1399862 original size:21 final size:21
Alignment explanation
Indices: 1399813--1399907 Score: 77
Period size: 21 Copynumber: 4.3 Consensus size: 21
1399803 TGAGTGCATT
* *
1399813 GATGCACATTCAAGGAGTGCATC
1 GATGCACATTC-ATGA-TGTATC
*
1399836 GGTGCATC-TTCATGATGTATC
1 GATGCA-CATTCATGATGTATC
*
1399857 GATGCACATTCATATGGATGCATC
1 GATGCACATTC--AT-GATGTATC
1399881 GATGCACATTCAT-AGTGTATC
1 GATGCACATTCATGA-TGTATC
1399902 GATGCA
1 GATGCA
1399908 TTATGCACAA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
20 2 0.03
21 24 0.40
22 5 0.08
23 10 0.17
24 19 0.32
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (21 bp):
GATGCACATTCATGATGTATC
Found at i:1399893 original size:45 final size:44
Alignment explanation
Indices: 1399813--1399907 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 44
1399803 TGAGTGCATT
*
1399813 GATGCACATTCAAGGAGTGCATCGGTGCATCTTCAT-GATGTATC
1 GATGCACATTCAAGGAGTGCATCGATGCATCTTCATAG-TGTATC
1399857 GATGCACATTCATATGGA-TGCATCGATGCA-CATTCATAGTGTATC
1 GATGCACATTCA-A-GGAGTGCATCGATGCATC-TTCATAGTGTATC
1399902 GATGCA
1 GATGCA
1399908 TTATGCACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
44 13 0.28
45 29 0.63
46 4 0.09
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (44 bp):
GATGCACATTCAAGGAGTGCATCGATGCATCTTCATAGTGTATC
Found at i:1399894 original size:24 final size:23
Alignment explanation
Indices: 1399807--1399892 Score: 90
Period size: 24 Copynumber: 3.8 Consensus size: 23
1399797 CACTGCTGAG
*
1399807 TGCATTGATGCACATTCAA-GGA
1 TGCATCGATGCACATTCAATGGA
*
1399829 GTGCATCGGTGCATC-TTC-AT-GA
1 -TGCATCGATGCA-CATTCAATGGA
*
1399851 TGTATCGATGCACATTCATATGGA
1 TGCATCGATGCACATTCA-ATGGA
1399875 TGCATCGATGCACATTCA
1 TGCATCGATGCACATTCA
1399893 TAGTGTATCG
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 1 0.02
21 13 0.25
22 3 0.06
23 15 0.29
24 20 0.38
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (23 bp):
TGCATCGATGCACATTCAATGGA
Found at i:1405599 original size:21 final size:21
Alignment explanation
Indices: 1405544--1405599 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1405534 GAGAGCGTGT
* *
1405544 GTGCATTGATGCACAGTCAAG
1 GTGCATCGATGCATAGTCAAG
1405565 GTGCATCGATGCATAGTCAAG
1 GTGCATCGATGCATAGTCAAG
1405586 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1405600 CAAGTGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATAGTCAAG
Found at i:1405774 original size:65 final size:65
Alignment explanation
Indices: 1405659--1405783 Score: 191
Period size: 65 Copynumber: 1.9 Consensus size: 65
1405649 TGCACTAAGG
*
1405659 GTGCATCGATGCATAAATTGCATTCGATGTTTCAAACAATCCTGGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAATCCTGGAGTGCATCGATGCATGGTAT
* *
1405724 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAA-AATAGCT-GAGGTGCATCGATGCAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAT-CCTGGA-GTGCATCGATGCAT
1405784 TGCTTATGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
64 5 0.09
65 50 0.91
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAATCCTGGAGTGCATCGATGCATGGTAT
Found at i:1405794 original size:65 final size:65
Alignment explanation
Indices: 1405660--1405815 Score: 185
Period size: 65 Copynumber: 2.4 Consensus size: 65
1405650 GCACTAAGGG
* * *
1405660 TGCATCGATGCATAAATTGCATTCGATGTTTCAAACAATCCTGGAGTGCATCGATGCATGGTATG
1 TGCATCGATGCATAAAATGCATTCGATGTTTCAAACAATCCTGGAGTGCATCGATGCATGCTATA
* *
1405725 TGCATCGATGCATAAAATGCATTCGATGTTTTAAA-AATAGCT-GAGGTGCATCGATGCATTGCT
1 TGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAT-CCTGGA-GTGCATCGATGCA-TGCT
1405788 -TA
63 ATA
* *
1405790 TGCATCGGTACACT-AAATGCATTCGA
1 TGCATCGATGCA-TAAAATGCATTCGA
1405816 AATTCAATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
64 5 0.06
65 71 0.89
66 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTCAAACAATCCTGGAGTGCATCGATGCATGCTATA
Found at i:1411488 original size:32 final size:32
Alignment explanation
Indices: 1411429--1411490 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1411419 AAAGTAGAGG
* *
1411429 GAATATTTTTTTTAATTTAATTATAATTTTGA
1 GAATATTTTTTTCAATATAATTATAATTTTGA
*
1411461 GAATA-TTTTTTCAATATAATTTTTAATTTT
1 GAATATTTTTTTCAATATAA-TTATAATTTT
1411491 TAATTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (32 bp):
GAATATTTTTTTCAATATAATTATAATTTTGA
Found at i:1411499 original size:19 final size:19
Alignment explanation
Indices: 1411467--1411514 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
1411457 TTGAGAATAT
*
1411467 TTTTTCAATATAATTTTTAA
1 TTTTT-AATATAATTATTAA
*
1411487 TTTTTAATTTAATTATTAA
1 TTTTTAATATAATTATTAA
1411506 TATTTTAAT
1 T-TTTTAAT
1411515 CATATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAATATAATTATTAA
Found at i:1413755 original size:41 final size:40
Alignment explanation
Indices: 1413704--1413804 Score: 132
Period size: 40 Copynumber: 2.5 Consensus size: 40
1413694 CAACCCAGGT
* * *
1413704 TCCAAATTCGCAATGTGATTTTAAGATTCGCAATGCGATAG
1 TCCAAATTCGCAATGCGA-TTTAAGATTCGCAACGCGATAC
* *
1413745 TCGAAATTCGCAACGCGATTTAAGATTCGCAACGCGATAC
1 TCCAAATTCGCAATGCGATTTAAGATTCGCAACGCGATAC
*
1413785 TCCAAAATCGCAATGC-ATTT
1 TCCAAATTCGCAATGCGATTT
1413805 GTTTCTTAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 4 0.08
40 33 0.63
41 15 0.29
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (40 bp):
TCCAAATTCGCAATGCGATTTAAGATTCGCAACGCGATAC
Found at i:1413774 original size:19 final size:19
Alignment explanation
Indices: 1413709--1413782 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
1413699 CAGGTTCCAA
* *
1413709 ATTCGCAATGTGATTTTAAG
1 ATTCGCAACGCGA-TTTAAG
* *
1413729 ATTCGCAATGCGATAGTCGAA-
1 ATTCGCAACGCGAT--T-TAAG
1413750 ATTCGCAACGCGATTTAAG
1 ATTCGCAACGCGATTTAAG
1413769 ATTCGCAACGCGAT
1 ATTCGCAACGCGAT
1413783 ACTCCAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 2 0.04
19 16 0.35
20 12 0.26
21 14 0.30
22 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (19 bp):
ATTCGCAACGCGATTTAAG
Found at i:1414758 original size:21 final size:21
Alignment explanation
Indices: 1414732--1414826 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 21
1414722 AACAAATGCA
* *
1414732 TTGCGATTTTGGAGTACCGTG
1 TTGCGATTTTGGACTATCGTG
*
1414753 TTGCGAATTTT-GACTATCGCG
1 TTGCG-ATTTTGGACTATCGTG
1414774 TTGCGATTTTGGACTATCGTG
1 TTGCGATTTTGGACTATCGTG
* * * *
1414795 TTGCGAATTTCGACTTTCGCG
1 TTGCGATTTTGGACTATCGTG
*
1414816 TTGCGAATTTG
1 TTGCGATTTTG
1414827 ACTTTCACGT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
20 5 0.08
21 53 0.84
22 5 0.08
ACGTcount: A:0.16, C:0.17, G:0.27, T:0.40
Consensus pattern (21 bp):
TTGCGATTTTGGACTATCGTG
Found at i:1414795 original size:42 final size:42
Alignment explanation
Indices: 1414732--1414845 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 42
1414722 AACAAATGCA
* * *
1414732 TTGCGATTTTGGAGTACCGTGTTGCGAATTTTGACTATCGCG
1 TTGCGATTTTGGACTATCGTGTTGCGAATTTCGACTATCGCG
*
1414774 TTGCGATTTTGGACTATCGTGTTGCGAATTTCGACTTTCGCG
1 TTGCGATTTTGGACTATCGTGTTGCGAATTTCGACTATCGCG
* * **
1414816 TTGCGAATTT-GACTTTCACGTTGCGAATTT
1 TTGCGATTTTGGACTATCGTGTTGCGAATTT
1414846 AGAACCTGGG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 17 0.27
42 47 0.73
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.40
Consensus pattern (42 bp):
TTGCGATTTTGGACTATCGTGTTGCGAATTTCGACTATCGCG
Found at i:1414842 original size:20 final size:21
Alignment explanation
Indices: 1414752--1414904 Score: 122
Period size: 21 Copynumber: 7.5 Consensus size: 21
1414742 GGAGTACCGT
*
1414752 GTTGCGAATTTTGACTATCGC
1 GTTGCGAATTTCGACTATCGC
* * *
1414773 GTTGCGATTTTGGACTATCGT
1 GTTGCGAATTTCGACTATCGC
*
1414794 GTTGCGAATTTCGACTTTCGC
1 GTTGCGAATTTCGACTATCGC
* *
1414815 GTTGCGAATTT-GACTTTCAC
1 GTTGCGAATTTCGACTATCGC
* * *
1414835 GTTGCGAATTTAGA--ACCTGG
1 GTTGCGAATTTCGACTATC-GC
*
1414855 GTTGCGAAATTT-GAAT-TCGC
1 GTTGCG-AATTTCGACTATCGC
* *
1414875 GTTGCGAATTT-GA-GATCGT
1 GTTGCGAATTTCGACTATCGC
1414894 GTTGCGAATTT
1 GTTGCGAATTT
1414905 GTTGGTCATT
Statistics
Matches: 110, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
19 22 0.20
20 34 0.31
21 54 0.49
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (21 bp):
GTTGCGAATTTCGACTATCGC
Found at i:1418986 original size:17 final size:16
Alignment explanation
Indices: 1418960--1418993 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1418950 CGTTGTAAGG
1418960 TAATTTTTTTAATATA
1 TAATTTTTTTAATATA
*
1418976 TAATATTTTTTTATATA
1 TAAT-TTTTTTAATATA
1418993 T
1 T
1418994 GATTATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTTTTAATATA
Found at i:1426328 original size:32 final size:32
Alignment explanation
Indices: 1426282--1426391 Score: 121
Period size: 32 Copynumber: 3.7 Consensus size: 32
1426272 TAGCGAGGTC
*
1426282 GACAAAGTCGAGTGGTTGGGTGAGTAGAATTT
1 GACAAAGTCAAGTGGTTGGGTGAGTAGAATTT
*
1426314 GACAAAGTCAAGTGG-T---T--G--G-ATTC
1 GACAAAGTCAAGTGGTTGGGTGAGTAGAATTT
* *
1426337 AACAGAGTCAAGTGGTTGGGTGAGTAGAATTT
1 GACAAAGTCAAGTGGTTGGGTGAGTAGAATTT
1426369 GACAAAGTCAAGTGGTTGGGTGA
1 GACAAAGTCAAGTGGTTGGGTGA
1426392 ATCGGATGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
23 16 0.26
24 2 0.03
26 1 0.02
27 1 0.02
28 1 0.02
29 1 0.02
31 2 0.03
32 38 0.61
ACGTcount: A:0.30, C:0.08, G:0.35, T:0.26
Consensus pattern (32 bp):
GACAAAGTCAAGTGGTTGGGTGAGTAGAATTT
Found at i:1429203 original size:31 final size:31
Alignment explanation
Indices: 1429168--1429234 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1429158 TTAAAATACA
1429168 TAAGATATGACCACTTACATTTTTATTTAAT
1 TAAGATATGACCACTTACATTTTTATTTAAT
* ***
1429199 TAAGATATGATCACTTTTGTTTTTATTTAAT
1 TAAGATATGACCACTTACATTTTTATTTAAT
1429230 TAAGA
1 TAAGA
1429235 CGTGGTCACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (31 bp):
TAAGATATGACCACTTACATTTTTATTTAAT
Found at i:1430673 original size:43 final size:44
Alignment explanation
Indices: 1430626--1430762 Score: 131
Period size: 43 Copynumber: 3.2 Consensus size: 44
1430616 TGACAACATA
*
1430626 TAGCGGCGATTGTTCA-ACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGATTGTTCAGACAAACGCCGCAATAGGTATTGATATT
* * * * * *
1430669 TAGCGGCGTTTG-GCATAAAAACGACGCAATAGGTGTTGATATT
1 TAGCGGCGATTGTTCAGACAAACGCCGCAATAGGTATTGATATT
* * *
1430712 TAACGGC-ATT-TGACAGACAAACGCCGCAATA-GTCATTGATGTT
1 TAGCGGCGATTGT-TCAGACAAACGCCGCAATAGGT-ATTGATATT
1430755 TAGCGGCG
1 TAGCGGCG
1430763 TTTTCTTCAC
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
42 6 0.08
43 68 0.92
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (44 bp):
TAGCGGCGATTGTTCAGACAAACGCCGCAATAGGTATTGATATT
Found at i:1430775 original size:43 final size:43
Alignment explanation
Indices: 1430642--1430825 Score: 120
Period size: 43 Copynumber: 4.3 Consensus size: 43
1430632 CGATTGTTCA
* * * * ** *
1430642 ACAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTGGCAT
1 ACAAACGCCGCAATAGATATTGATGTTTACCGGCGTTTTTCCT
* * * * * * * ** **
1430685 AAAAACGACGCAATAGGTGTTGATATTTAACGGCATTTGACAG
1 ACAAACGCCGCAATAGATATTGATGTTTACCGGCGTTTTTCCT
* *
1430728 ACAAACGCCGCAATAG-TCATTGATGTTTAGCGGCG-TTTTCTT
1 ACAAACGCCGCAATAGAT-ATTGATGTTTACCGGCGTTTTTCCT
* * * *
1430770 CACAAACGCCGCAGTAGATGTTTATTTTTACCGGCGTTTTTCCT
1 -ACAAACGCCGCAATAGATATTGATGTTTACCGGCGTTTTTCCT
1430814 ACAAACGCCGCA
1 ACAAACGCCGCA
1430826 GAATATGTCT
Statistics
Matches: 113, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
42 4 0.04
43 102 0.90
44 7 0.06
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (43 bp):
ACAAACGCCGCAATAGATATTGATGTTTACCGGCGTTTTTCCT
Found at i:1430863 original size:45 final size:42
Alignment explanation
Indices: 1430758--1430869 Score: 109
Period size: 43 Copynumber: 2.5 Consensus size: 42
1430748 TGATGTTTAG
* * *
1430758 CGGCGTTTTCTTCACAAACGCCGCAGTAGATGTTTATTTTTAC
1 CGGCGTTTT-TTCACAAACGCCGCAGAAGATGTTTAATTTCAC
* *
1430801 CGGCGTTTTTCCTACAAACGCCGCAGAATATGTCTTGAGATTTCA-
1 CGGCGTTTTTTC-ACAAACGCCGCAGAAGATGT-TT-A-ATTTCAC
*
1430846 CGGCGTTTTTATCACAAACCCCGC
1 CGGCGTTTTT-TCACAAACGCCGC
1430870 TAAATGTATG
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
42 2 0.04
43 27 0.47
44 2 0.04
45 21 0.37
46 5 0.09
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (42 bp):
CGGCGTTTTTTCACAAACGCCGCAGAAGATGTTTAATTTCAC
Found at i:1431256 original size:23 final size:21
Alignment explanation
Indices: 1431210--1431263 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1431200 ATATATTACT
*
1431210 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
* *
1431231 TCTCTCTGTGCTGTCGCTGCT
1 TCTCTCTGTGCTGCCGCTGCC
*
1431252 TCTCTCTCTGCT
1 TCTCTCTGTGCT
1431264 TTCGCTACTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.00, C:0.39, G:0.19, T:0.43
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTGCC
Found at i:1431268 original size:21 final size:21
Alignment explanation
Indices: 1431224--1431316 Score: 71
Period size: 21 Copynumber: 4.4 Consensus size: 21
1431214 TCTGTTCTGC
* * *
1431224 CGCTGCCTCTCTCTGTGCTGT
1 CGCTGCTTCTCTCTCTGCTTT
1431245 CGCTGCTTCTCTCTCTGCTTT
1 CGCTGCTTCTCTCTCTGCTTT
* * ** *
1431266 CGCTACTGCTCTAGCTGCTTC
1 CGCTGCTTCTCTCTCTGCTTT
* *
1431287 CACTGCTGCTCTCTCTG-TTT
1 CGCTGCTTCTCTCTCTGCTTT
*
1431307 CCCTTGCTTC
1 CGC-TGCTTC
1431317 ATTTTTCGCT
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
20 4 0.07
21 52 0.93
ACGTcount: A:0.03, C:0.39, G:0.17, T:0.41
Consensus pattern (21 bp):
CGCTGCTTCTCTCTCTGCTTT
Found at i:1439947 original size:41 final size:42
Alignment explanation
Indices: 1439880--1440000 Score: 167
Period size: 41 Copynumber: 3.0 Consensus size: 42
1439870 CGTTTATACA
*
1439880 AAAAAACGCCACCATTGATT-ATACTATTGTGGCGTTTGT-T
1 AAAAAACGCCACTATTGATTAATACTATTGTGGCGTTTGTCT
* * *
1439920 AAAAAACGCCACTATTGATTAAAACTATTGTAGCGTTTATCT
1 AAAAAACGCCACTATTGATTAATACTATTGTGGCGTTTGTCT
**
1439962 -AAAAACGCCACTATTGATTAATACTATTACGGCGTTTGT
1 AAAAAACGCCACTATTGATTAATACTATTGTGGCGTTTGT
1440001 GGTATAAATG
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 19 0.27
41 50 0.71
42 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (42 bp):
AAAAAACGCCACTATTGATTAATACTATTGTGGCGTTTGTCT
Found at i:1443949 original size:125 final size:125
Alignment explanation
Indices: 1443727--1443977 Score: 502
Period size: 125 Copynumber: 2.0 Consensus size: 125
1443717 ACGTAATTTA
1443727 TAAGGCGGTTGCAAAACTCATTGTAAACCGGTTGAAGCCACTTCTTCCACCATGGGTGGTAGAAA
1 TAAGGCGGTTGCAAAACTCATTGTAAACCGGTTGAAGCCACTTCTTCCACCATGGGTGGTAGAAA
1443792 ACCAAACTAGTTTTGTGCCGGGACGATCAATTGTTGATAATATCATTCTCGCCCAGGAGG
66 ACCAAACTAGTTTTGTGCCGGGACGATCAATTGTTGATAATATCATTCTCGCCCAGGAGG
1443852 TAAGGCGGTTGCAAAACTCATTGTAAACCGGTTGAAGCCACTTCTTCCACCATGGGTGGTAGAAA
1 TAAGGCGGTTGCAAAACTCATTGTAAACCGGTTGAAGCCACTTCTTCCACCATGGGTGGTAGAAA
1443917 ACCAAACTAGTTTTGTGCCGGGACGATCAATTGTTGATAATATCATTCTCGCCCAGGAGG
66 ACCAAACTAGTTTTGTGCCGGGACGATCAATTGTTGATAATATCATTCTCGCCCAGGAGG
1443977 T
1 T
1443978 TTTTCACTTT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (125 bp):
TAAGGCGGTTGCAAAACTCATTGTAAACCGGTTGAAGCCACTTCTTCCACCATGGGTGGTAGAAA
ACCAAACTAGTTTTGTGCCGGGACGATCAATTGTTGATAATATCATTCTCGCCCAGGAGG
Found at i:1445702 original size:21 final size:23
Alignment explanation
Indices: 1445676--1445733 Score: 84
Period size: 21 Copynumber: 2.5 Consensus size: 23
1445666 GATAATTGGG
1445676 ATATTAACTTAAAATATA-TTT-
1 ATATTAACTTAAAATATATTTTA
1445697 ATATTAACTTATTAAATATATTTTA
1 ATATTAACTTA--AAATATATTTTA
1445722 ATATTAACTTAA
1 ATATTAACTTAA
1445734 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.33
23 8 0.24
24 3 0.09
25 11 0.33
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTAACTTAAAATATATTTTA
Found at i:1445725 original size:25 final size:25
Alignment explanation
Indices: 1445676--1445748 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 25
1445666 GATAATTGGG
1445676 ATATTAACTTA--AAATATA-TTT-
1 ATATTAACTTATTAAATATATTTTA
1445697 ATATTAACTTATTAAATATATTTTA
1 ATATTAACTTATTAAATATATTTTA
*
1445722 ATATTAACTTAATTTAAAAATATTTTA
1 ATATTAACTT-A-TTAAATATATTTTA
1445749 TTTTATTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
21 11 0.24
23 7 0.16
24 3 0.07
25 10 0.22
26 1 0.02
27 13 0.29
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATTAACTTATTAAATATATTTTA
Found at i:1445746 original size:27 final size:25
Alignment explanation
Indices: 1445686--1445748 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 25
1445676 ATATTAACTT
1445686 AAAATATATTT-ATATTAACTTATTA
1 AAAATAT-TTTAATATTAACTTATTA
*
1445711 AATATATTTTAATATTAACTTAATTTA
1 AAAATATTTTAATATTAACTT-A-TTA
1445738 AAAATATTTTA
1 AAAATATTTTA
1445749 TTTTATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 3 0.09
25 16 0.48
26 1 0.03
27 13 0.39
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATATTTTAATATTAACTTATTA
Found at i:1447906 original size:14 final size:15
Alignment explanation
Indices: 1447879--1447915 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1447869 ATAAATTAGT
1447879 TAAAA-ATTTAAAAA
1 TAAAATATTTAAAAA
*
1447893 TAAATTATTT-AAAA
1 TAAAATATTTAAAAA
1447907 TAAAATATT
1 TAAAATATT
1447916 AATTACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAAAA
Found at i:1452763 original size:3 final size:3
Alignment explanation
Indices: 1452755--1452840 Score: 156
Period size: 3 Copynumber: 29.0 Consensus size: 3
1452745 AATATTTATT
*
1452755 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1452802 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1452841 AAGCAAACTG
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
2 2 0.02
3 79 0.98
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1454223 original size:16 final size:16
Alignment explanation
Indices: 1454202--1454232 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1454192 ATAAATAAAT
1454202 GAACATAAACGAACAC
1 GAACATAAACGAACAC
1454218 GAACATAAACGAACA
1 GAACATAAACGAACA
1454233 TAAACGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:1454959 original size:13 final size:13
Alignment explanation
Indices: 1454941--1454994 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
1454931 AATGAACATA
1454941 AACGAACATAACC
1 AACGAACATAACC
1454954 AACGAACAT-A--
1 AACGAACATAACC
*
1454964 AACGAAC-TAACTG
1 AACGAACATAAC-C
1454977 AACGAACATAACC
1 AACGAACATAACC
1454990 GAACG
1 -AACG
1454995 TTCACGAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
9 1 0.03
10 8 0.24
12 1 0.03
13 16 0.47
14 8 0.24
ACGTcount: A:0.52, C:0.26, G:0.13, T:0.09
Consensus pattern (13 bp):
AACGAACATAACC
Found at i:1454963 original size:23 final size:23
Alignment explanation
Indices: 1454934--1454993 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
1454924 ATAAATGAAT
1454934 GAACATAAACGAACATAAC-CAAC
1 GAACATAAACGAAC-TAACTCAAC
*
1454957 GAACATAAACGAACTAACTGAAC
1 GAACATAAACGAACTAACTCAAC
*
1454980 GAACATAACCGAAC
1 GAACATAAACGAAC
1454994 GTTCACGAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 4 0.12
23 30 0.88
ACGTcount: A:0.53, C:0.25, G:0.12, T:0.10
Consensus pattern (23 bp):
GAACATAAACGAACTAACTCAAC
Found at i:1455305 original size:14 final size:14
Alignment explanation
Indices: 1455288--1455344 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
1455278 GAATGAACAT
1455288 AAACGAACATAACC
1 AAACGAACATAACC
1455302 AAACGAACAT----
1 AAACGAACATAACC
*
1455312 AAACGAACATAACT
1 AAACGAACATAACC
*
1455326 GAACGAACATAACC
1 AAACGAACATAACC
*
1455340 GAACG
1 AAACG
1455345 TTCACGAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 10 0.27
14 27 0.73
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:1455354 original size:24 final size:24
Alignment explanation
Indices: 1455269--1455343 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
1455259 GATTGGGTTA
* *
1455269 AACATAAATGAATGAACATAAACG
1 AACATAACTGAACGAACATAAACG
**
1455293 AACATAACCAAACGAACATAAACG
1 AACATAACTGAACGAACATAAACG
*
1455317 AACATAACTGAACGAACATAACCG
1 AACATAACTGAACGAACATAAACG
1455341 AAC
1 AAC
1455344 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAACTGAACGAACATAAACG
Found at i:1455441 original size:347 final size:348
Alignment explanation
Indices: 1454773--1455477 Score: 1310
Period size: 351 Copynumber: 2.0 Consensus size: 348
1454763 CTTATGGATC
1454773 GTTCAAAAAGAACTAAACCATGTTAATATGTGGGTTTTCCAAATAAAATTGGCTTAATTATGGAG
1 GTTCAAAAAGAACTAAACCATGTTAATATGTGGGTTTTCCAAATAAAATTGGCTTAATTATGGAG
1454838 TTGGTTATCAGAATATCAGATTAATTAATATTTTTAAGATACTTACAAATTGGTCACCAAATTGA
66 TTGGTTATCAGAATATCAGATTAATTAATATTTTTAAGATACTTACAAATTGGTCACCAAATTGA
1454903 TTTAAGAAGATTGGGTTAAACATAAATGAATGAACATAAACGAACATAACCAACGAACATAAACG
131 TTTAAGAAGATTGGGTTAAACATAAATGAATGAACATAAACGAACATAACCAACGAACATAAACG
1454968 AACTAACTGAACGAACATAACCGAACGTTCACGAACGTAATGAACGAACGAGACCTATGTTCATG
196 AACTAACTGAACGAACATAACCGAACGTTCACGAACGTAATGAACGAACGAGACCTATGTTCATG
1455033 TTCGTTCATTTAATTAAACGATCACAAAATCTTGTTCATGTTCGTTCATTTAATAAATAAATGCA
261 TTCGTTCATTTAATTAAACGATCACAAAATCTTGTTCATGTTCGTTCATTT-ATAAATAAATGCA
1455098 TAT-AA-G-ACTTCCC-CCGCACG
325 TATAAACGAACTTCCCGCCGCACG
1455118 GTTCAAAAAGAACTAAACCATGTTAATATTGTTGGGTTTTCCAAATAAAATTGGCTTAATTATGG
1 GTTCAAAAAGAACTAAACCATGTTAATA-TG-TGGGTTTTCCAAATAAAATTGGCTTAATTATGG
1455183 AGTTGGTTATCAGAATATCAGATTAATTAATATTTTTAAGATACTTACAAATTGGTCACCAAAAT
64 AGTTGGTTATCAGAATATCAGATTAATTAATATTTTTAAGATACTTACAAATTGGTCACC-AAAT
1455248 TGATTTAAGAAGATTGGGTTAAACATAAATGAATGAACATAAACGAACATAACCAAACGAACATA
128 TGATTTAAGAAGATTGGGTTAAACATAAATGAATGAACATAAACGAACATAACC-AACGAACATA
1455313 AACGAACATAACTGAACGAACATAACCGAACGTTCACGAACGTAAATGAACGAACGAGACCTATG
192 AACGAAC-TAACTGAACGAACATAACCGAACGTTCACGAACGT-AATGAACGAACGAGACCTATG
1455378 TTCATGTTCGTTCATTTAATTAAACGATCACAAAATCTTGTTCATGTTCGTTCATTTAATAAATA
255 TTCATGTTCGTTCATTTAATTAAACGATCACAAAATCTTGTTCATGTTCGTTCATTT-ATAAATA
1455443 AATGCATATAAACGAACTTCCCGCCGCACG
319 AATGCATATAAACGAACTTCCCGCCGCACG
1455473 GTTCA
1 GTTCA
1455478 TGAACGGTTC
Statistics
Matches: 350, Mismatches: 0, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
345 28 0.08
346 2 0.01
347 93 0.27
348 58 0.17
349 17 0.05
350 35 0.10
351 95 0.27
352 2 0.01
353 1 0.00
354 7 0.02
355 12 0.03
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (348 bp):
GTTCAAAAAGAACTAAACCATGTTAATATGTGGGTTTTCCAAATAAAATTGGCTTAATTATGGAG
TTGGTTATCAGAATATCAGATTAATTAATATTTTTAAGATACTTACAAATTGGTCACCAAATTGA
TTTAAGAAGATTGGGTTAAACATAAATGAATGAACATAAACGAACATAACCAACGAACATAAACG
AACTAACTGAACGAACATAACCGAACGTTCACGAACGTAATGAACGAACGAGACCTATGTTCATG
TTCGTTCATTTAATTAAACGATCACAAAATCTTGTTCATGTTCGTTCATTTATAAATAAATGCAT
ATAAACGAACTTCCCGCCGCACG
Found at i:1455567 original size:2 final size:2
Alignment explanation
Indices: 1455560--1455598 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1455550 TTAAAGCTCT
1455560 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1455599 TTCATGTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1455803 original size:2 final size:2
Alignment explanation
Indices: 1455798--1455823 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1455788 TTTTTATTTA
1455798 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1455824 TAGGTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1461927 original size:23 final size:23
Alignment explanation
Indices: 1461900--1461963 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
1461890 CAATAAAGCA
1461900 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATAAACG
*
1461923 CTACCTATTACATTATATAAGCG
1 CTACCTATTACATTATATAAACG
*
1461946 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
1461964 TTTTACCTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Done.